1b.Approach (from AD-416)
Develop and release improved apple rootstocks. Perform all breeding and evaluation stages involved in the 15-25 year process of developing new rootstocks with the assistance of recently developed breeding tools, such as marker-assisted selection. Develop improved propagation methods that speed the distribution of selected material to customers through established networks of cooperating nurseries. Exogenous treatments of layering propagation stool beds will increase adventitious root formation and quality of nursery liners. Incorporate innovative concepts of orchard establishment and management including mechanization. Existing experimental rootstocks in the breeding pipeline possess adaptations for novel orchard concepts and mechanization. Develop and apply genomic and bioinformatic tools to marker-assisted selection of apple rootstocks. Develop algorithms to assist with identifying specific markers for priority horticultural traits from the large body of expressed sequence tags (EST) and genomic sequence data now available.

3.Progress Report
The program is well on its way to achieving one of its major technology transfer goals: the propagation and planting of three million apple rootstocks/year carrying the Geneva trademark symbolizing increased disease resistance and productivity. The number of micropropagation nurseries that are generating plants for the industry has increased from two to five and the eight major apple rootstock nurseries are planting new stool beds to satisfy the industry’s needs. All production of Geneva rootstock material has been sold out for 2008, 2009, 2010 and 2011, a sign that technology transfer from the program and from cooperating institutions is getting through to industry and having a positive effect. All routine operations involved with breeding apple rootstocks such as planting new orchards, measuring tree size and productivity, measuring tolerance to diseases such as fire blight, describing propagation properties, making new experimental trees in the nursery, making new crosses, harvesting and grading rootstock liners, etc. were successful with the exception of some problems probably caused by the improper application of a pre emergence herbicide that is routinely used in our breeding program, where the Field Research Unit of Cornell (the only people trained and equipped to apply the material) used the powder form of the herbicide instead of the liquid form that is generally used. This caused quite a bit of stunting and plant loss in the new stool beds that we were trying to establish for propagation research.

Continued a major effort into diagnostic DNA fingerprinting of apple rootstocks for proper identification of misidentified rootstocks and avoidance of potential downstream planting and propagation problems.

Collaborated with PI to characterize tolerance/resistance to components of the Apple Replant Disease (ARD) and sent the population segregating for tolerance/resistance to his laboratory to be tested with individual components implicated in ARD (such as Rhizoctonia and Pythium) to check for co segregation of resistance with mapped molecular markers.

Completed a major replicated experiment where most seedling from crosses made from 2002-2008 were planted in a replicated fashion and challenged with Phytophthora root rot to gauge the heritability components and the best parental combinations for that disease. We also wanted to gauge what type of segregation for resistance to Phytophthora each cross had to determine whether it is possible to start a molecular study to identify the genetic components behind the resistance with the longer term goal of developing Marker Aided Selection for this trait as well.

Initiated collaboration with Cornell Geneva Hort. Sciences. Have identified several genes involved with water stress and submergence tolerance and screened the apple rootstock BAC library and identified several clones with the genomic sequences of these stress response genes.

4.Accomplishments
1.
Apple Rootstock Map Ready for Publication: Genetic maps are an important prerequisite to the discovery of genomic regions that affect apple rootstock traits. We completed and prepared for publication a genetic map of apple rootstocks that encompasses all 17 linkage groups (chromosomes) of the apple genome and identified the location of 16 genes expressed in roots only and 13 disease resistance homologues some of which co-locate to known disease resistance regions in apple rootstocks. This accomplishment has enabled the discovery of markers linked to important apple rootstock traits in preparation for Marker Assisted Breeding.

2.
Discovery of a Secondary Gene for Powdery Mildew Resistance: Resistance to powdery mildew in apple rootstocks is a desirable nursery trait. We have discovered and submitted to peer-reviewed publication the location of a secondary gene that affects disease resistance to powdery mildew. This gene is located on linkage group 7 of apple. This accomplishment has elucidated the need for an additional marker to be used in Marker Assisted Breeding for Powdery Mildew resistance and explained the inconsistencies of published results based on a one gene model for the resistance.

3.
Discovery of Novel Root Morphologies in Apple Rootstocks: Very little is known about how the morphology of a root system affects field performance of a rootstock. By imaging hundreds of root systems of young trees and subsequent analysis of those images with specialized software, we have discovered root morphological characters that may allow apple rootstocks to penetrate, anchor and explore the soil profile more efficiently than current commercial rootstocks. This research will aid in the selection and development of improved apple rootstock cultivars.

4.
Completion of a Five Year Field Study of Tolerance to Apple Replant Disease: Yield loss caused Apple Replant Disease is a very important problem for apple growers. We have completed 5 years of testing of Geneva rootstocks in three apple replant replicated organic and conventional field plots in Washington State. This research is being compiled for publication for lay press and scientific journals. It identifies Geneva apple rootstocks G.41 and G.41 and G.4214 as the best options be used in conventional and organic orchards suffering from replant disease. It also identifies really bad rootstocks for replant situations. The discovery of new rootstocks that can be used in Apple Replant soils with minimal yield loss will allow growers and the apple industry to maintain production on good orchard land that has been marginalized because of ARD. The application of this knowledge has a large potential impact on the Apple Industry.

5.
Pre-Release Increase of Plant Material for Commercial Production: The transition from an improved apple rootstock research line to a commercial cultivar may take several years because of the inherent high establishment costs of new propagation beds and the slow propagation cycles. In preparation for the pending release of three new yield-efficient, dwarfing and semi-dwarfing disease resistant apple rootstocks well adapted to Washington state, New York apple growing regions we have initiated micropropagation and pre commercial production of 5,000 plants per rootstock of 4 new apple rootstocks. Making larger amounts of plants available to the nursery industry will make a larger impact on the apple industry much sooner than by the increase of plant material using conventional methods.